Mutant superbug threat to SA poultry

Chickens feeding on a chicken farm.
Image: JAMES OATWAY / SUNDAY TIMES

Superbugs with an alarming gene have been found in South Africa in sick and dead poultry.

The bacteria are resistant to colistin, a last-resort antibiotic for humans, and have been multiplying rapidly in South Africa since 2014. The discovery of the MCR-1 gene, which makes common bacteria resistant to colistin, has raised global concerns for human health.

The MCR-1 gene in the superbugs in South Africa - identified for the first time in November in poultry and pigs in China - poses no immediate threat to consumers, since diseased birds do not go onto the shelves.

South African Poultry Association senior executive Dr Charlotte Nkuna said companies tested their birds at slaughter and retailers did regular audits on their products.

"People are unlikely to pick up anything and poultry has a mandatory withdrawal period from antibiotics before they are sold," she said.

Resistant bacteria can spread to people through food and environmental contamination and humans can transmit them to animals.

In South Africa, the animal health company V-Tech - which has an antimicrobial resistance surveillance programme used by poultry producers, piggeries and feedlots - noted increasing colistin resistance but did not know the reason for this.

V-Tech CEO Johan Oosthuyse said: "There was a pattern of very low resistance to colistin, at about 2% to 4%, until about two years ago, when we started seeing resistance creeping up to just above 13%.

"As soon as The Lancet journal published the information about the gene, we took the resistant bacteria we had kept frozen and sent samples to the University of Bern in Switzerland." The first results came back in January: 19 out of 25 samples with colistin resistance had the MCR-1 gene. The second batch of results came back this week: eight out of 15 samples had the gene.

"That would mean that around 6% of the sick or dead birds tested had E coli bacteria with the MCR-1 gene," said Oosthuyse.

Professor Vincent Perreten at the Institute of Veterinary Bacteriology at the University of Bern who confirmed the MCR-1 gene in the samples, said the South African poultry industry was being proactive and courageous by sharing the results.

Theo Delport, MD of the poultry division for Astral, said: "For the past five to six years, sensitivity tests done on E colibacteria isolated from Astral's operation have shown that colistin was a drug of choice."

Veterinary microbiologist Moritz van Vuuren, professor emeritus at the University of Pretoria, said: "Bacteria resistant to colistin have always been present but the rate of resistance has increased, and, unfortunately, bacteria that carry mobile resistance genes against colistin."

The scientists who picked up the gene in China reported that it can spread easily from one strain of bacteria to another.

"The MCR-1 gene is already being transmitted between common bacteria such as E coli, which can cause urinary tract and many other types of infection, and Klebsiella pneumoniae, which causes pneumonia and other infections," Oosthuyse warned.

V-Tech has found lots of resistant bacteria among 4000 bacteria tested over the past five years but the colistin-resistant bacteria raised a red flag because colistin is critical in human medicine. In response to this threat, V-Tech stopped supplying colistin to farms where resistance to the antibiotic had been confirmed and it added routine scanning for the MCR-1 gene.

More than 60% of poultry producers in South Africa, including major producers such as Astral Foods, RLC Foods and Country Bird, use its surveillance programme.

Oosthuyse said: "A total ban on colistin use in animals will negatively impact meat production."

Registrar of medicines Dr Joey Gouws said colistin use in humans and animals had been discussed at meetings in November and February and the matter was complex.

"The council [Medicines Control Council] required additional work and investigations to allow for further discussions [at a meeting] in June," she said.

Department of Health spokesman Popo Maja said the department was very worried about antimicrobial resistance which, if not attended to, would become "an emerging catastrophe for human health".

The bacteria with the gene have been found mostly in animals, but some people have been infected too.

"Resistant bacteria or resistance genes can be transmitted from animals to humans, either through direct contact, the food chain or indirect environmental contact," said Van Vuuren.

Nkuna said producers and the veterinary fraternity were working to collect and centralise data on antimicrobial resistance and collaborating with the Health Department to preserve antibiotics for human and animal health.